Complicated
by Neferius
Summary: A single father meets a single mother, their three children get to know each other, and the relationships form. But just like anything in life, it's full of complications, hardships, and...simulator battles! Gendo x Kyoko – Asuka x Shinji x Rei.


**A/N: This story was spontaneously written a while back and really only needed an ending. This is an AU with a lot of OOC-ness ahead, so no complaining.**

* * *

**Complicated**

**Chapter One**

**New transfer**

**Fourteen years ago…**

Gendo looked down at the light blue bassinette and let out a sad sigh. He had a feeling this would happen eventually. He almost glared at the baby girl crying her eyes out for food. Gendo wanted to be mad at the child but it wasn't her fault and he knew it.

The built up frustration was finally released on the wall next to him when he punched it a few times until there was a good size hole and his hand ached. The crying increased, causing him to wake from his rage. He looked back down at the blue haired baby and picked her up. She wasn't even his child to begin with, but there he was, stroking her head and rocking her.

He left the room with the girl in his arms and walked into the kitchen where the bottle he had prepared sat waiting. He tested it on his wrist, the temperature was just right, and began feeding the little bundle in his arms.

He heard a thump on the ground next to him and smiled as his son, Shinji, picked himself up off the floor. Shinji may only be a year old but lately the boy was showing lots of concern for his new sister.

"It's okay Shinji, she's only hungry" he sat on their couch and Shinji soon followed. Gendo thought about the message he had received at work today. It had been from Yui and he had nearly broken down when he heard it.

"Hello Gendo, this is going to be hard for me to say, so I'll keep it simple" she had said it like she had been brooding over it for days but he knew better "I can't handle this relationship anymore and I'm moving out of the city" she coated it with a sweet voice but he knew that it was all a lie "I'm leaving Shinji and Rei in your care, I have a future ahead of me, and children will only hold me back. I'm sure you understand. Goodbye" he didn't know what he had seen in the manipulative woman.

A few tears leaked out of his eyes as he realized how bad his situation had become. He was a single father with two children, one of whom was the daughter of another man and he just started a new fulltime job at a pharmaceutical company named Nerv. How was he going to be able to balance work and family? He was calmed when he felt his son fall asleep; laying on his lap and his daughter's light suckling sounds.

He'd find a way, for these two children, his children.

* * *

"Dad get up" he heard a girls voice "come on daddy, you've got work" he slowly opened his eyes to find himself staring into two crimson orbs "Shinji has breakfast ready so get up old man" she jumped off of him and ran out of the room. Gendo sat up and looked at his clock, 6:45 it read, he turned to the side of the bed and got out of his comfortable paradise.

"Thank you Rei" Gendo said quietly as he headed for the shower.

Down the hall Shinji had just finished the eggs and was preparing some toast. It was simple but it fed everyone. He gasped as he suddenly felt two arms wrap around his chest.

"Good morning _onii-chan_" Rei whispered into his ear. He shrugged her off and greeted her.

"Morning Rei" he grabbed some toast and handed her a plate "here you go" she happily accepted the food and the two began to eat.

"So what are your plans for today, big brother" Rei asked as she munched on her toast.

"Me and the guys are going to the arcades after school and that's about it. How about you"?

"Mayumi and I have a class project due tomorrow so I'll be staying at school" she told him.

"Do you want me to pick you up?" he asked.

"I'd appreciated it. You wouldn't want your little sister to walk home all alone now would you?"

"Oh heavens no" Shinji answered sarcastically "I'd be too worried about you harming the goons that walked the streets. Somebody needs to protect them from danger" he grinned.

"Ha ha, very funny" she stuck her tongue out at him.

"Yeah yeah, I'll be there".

"Thanks, _onii-chan_" she smiled cheerfully.

"Now don't forget son" Gendo walked in, refreshed from his morning shower.

"I won't" Shinji grabbed his bag and handed Rei hers "We're going to school now, I'll see you later pops" the two children left the apartment and Gendo grabbed his breakfast.

As he ate, he thought about the last fourteen years. He still hasn't heard from Yui since she last left. It's not that he cared but he just figured that she might want to see her children at least once. Her loss he figured, they had both turned out better than he had ever wished. Gendo looked up at the clock and figured he should leave for work soon.

* * *

Gendo soon arrived at Nerv pharmaceuticals and parked in his spot close to the entrance, one of the perks to being a head scientist. He flashed his I.D. badge and security allowed him into the building. He walked into the main lobby where he met up with one of his colleagues.

"Good morning Naoko" he nodded to the brunet.

"Oh Gendo, just the man I wanted to see" Naoko waved him over and he soon complied "Gendo I'd like you to meet our newest addition" Naoko stepped aside and what appeared before Gendo could only be described as an angel. She had long, cinnamon colored hair and vibrant crystal blue eyes. She had fair skin and looked to be just a little younger than himself.

"It's a pleasure to finally meet you Dr. Rokubungi" she said with a slight German accent "I'm Kyoko Soryu, your new assistant" Gendo was so awestruck by the woman that he didn't realize he was staring. Naoko abruptly stepped on his foot while keeping a forced smile on her face.

"Oh ah, um, Hi…Kyoko, I'm Dr. Gendo Rokubungi" he fumbled with his words, causing Kyoko to chuckle and Naoko to roll her eyes. Naoko coughed into her hand, getting his attention.

"Why don't you show her the lab and get acquainted" she suggested.

"That sounds like an excellent idea" Kyoko mentioned as she clasped her hands together.

"Well um…follow me then" Gendo straightened out his lab coat let his new assistant to an elevator. Naoko watched curiously as the two descended into the lower depths of Nerv, a nervous look blossomed onto her face.

"Maybe this wasn't such a good idea" she thought as she remembered the look in both of their eyes.

* * *

"Class please settle down" Ms. Maya Ibuki asked nervously. The class ignored her. It wasn't exactly her fault, she was a new teacher "um, students…I have a…an announcement" this wasn't working for the young teacher, she just wasn't assertive enough. Shinji would say something but none of the students would listen to him and he knew it. Rei just didn't care as she stared out into the sky.

"Come on guys, that's enough" the class representative, Hikari Horaki, yelled out but got little response.

"Hey, Shut up" Touji Suzuhara shouted and everybody quieted down. He gave Hikari a quick nod, to which she smiled back. Kensuke grinned as he watched the two. The jock had calmed down since he asked Hikari out.

"That's better. Like I was saying, we have a new student today" this got everybody's attention "come on in" she told somebody at the door.

There were hushed whispers as a red headed bombshell entered the room. Every guy had their eyes glued to the girl's every asset, just imagining all the perverted things they could do.

"Hi everybody, my name is Asuka Soryu, it's a pleasure" she gave a slight bow and had a cheery smile on her face. Shinji was dumbstruck by the girl. He liked the way her light strawberry blond hair flowed smoothly down her back and how her beautiful sapphire eyes almost seemed to glow with life.

"Asuka was born here in Japan but moved to the United States for eight years and then to Germany for another six years" Maya told her class as she looked around the room and found what she was looking for "Shinji, can you raise your hand please" Shinji looked up at her with confusion written all over his face. He then remembered what she asked and rose his hand "Asuka, you can sit over there by Shinji".

"Okay" she said cheerfully. As she elegantly walked down the row of desks, she noticed all the girls frown at her and whisper to each other. Normally she wouldn't care, but a particular blue haired girl near the window was really unnerving her with her crimson eyed glare. She sat next to the boy named Shinji and gave him a friendly smile. He blushed and avoided her gaze, causing her to giggle. Though internally she was disappointed that he seemed to be like all the rest, she just wanted somebody normal to talk to for a change.

Shinji was trying to control himself since he never really talked to girls other than Rei and Hikari, but they were different. As Ms. Ibuki began her lecture Shinji struggled to think of something to say to the new student.

"So" he started "have you…been around campus yet" he asked but mentally kicked himself for such a dumb question. Asuka shook her head and whispered to him.

"No, I haven't yet" she was relieved that he had asked her that instead of 'do you have a boyfriend' or 'you want to have lunch together' like every other guy has in the past.

"Well…if you'd like I-I could show you around" he offered nervously.

"You know what, I'd like that" Asuka said as she gave him a genuine smile.

Mayumi heard a snap and turned her head to see Rei's pencil in two pieces.

"Uh oh" the bespectacled girl whispered.

* * *

Gendo allowed Kyoko to step through the doors first. She was surprised how big the room was.

"This is both my office and personal lab" he told her as she looked at all the computers and other equipment placed throughout the room.

"Amazing" she said in wonder as she walked around and lightly touched everything.

"It's nothing too great" Gendo said modestly while watching her every move.

"No, it is" she looked back at him "This is where you created _Conodrafin_, one of the greatest vaccines ever produced by Nerv" a light blush crossed her face as she noticed him checking her out.

"I did have some help" he stated as he took his eyes off of her. He looked around his office and found something to change the conversation "Would you like some Coffee or Tea" he asked.

"Tea please, but, I'm the assistant, let me get that" she walked over to a small table in the corner that Gendo was currently at. Their hands lightly touched as they tried to grab the same item. They both retracted the hands and smiled at each other.

* * *

Shinji, Kensuke, and Touji walked into the arcade with silly grins on their faces.

"You better watch your back Shinji, all the guys in class were pretty jealous that you were hanging out with Asuka all day" Kensuke warned his friend.

"Well, somebody had to show her around" Shinji said innocently as Touji shouted out.

"God I love this place" the arcade was their favorite hangout because of its wide variety of games. They had everything from table hockey to old school arcade games to full cockpit simulators. They saw a big crowd around their favorite simulator, Bio-Mech: Evangelion. It was not only a classic but the most played virtual battle simulator on the market. The three of them alone had unlocked numerous secret Evangelion's and weapons, at the cost of their allowance. As the three boys got closer to the machines, they saw just how big the crowd had actually gotten. The two simulators were surrounded by at least forty people.

The main video screen, centered between the machines, showed the two combatants squaring off. The first player was the reigning champ, Ichigo Konawa, using his customized Unit 13, with two rocket launchers strapped to its back and a giant Eva sized revolver in its right hand. The Unit was painted with hues of yellow and orange with a bit of black outlining. Shinji and Touji both knew they were better than the champ at the game but were too afraid of his entourage of goons to challenge him. They felt sorry for the poor fool that challenged him considering Ichigo was still quite good at the game. That's when they finally got a glimpse at the challengers Evangelion.

"No way, is that" Kensuke drooled "Is that Unit 04" Shinji was surprised to see that particular Evangelion in this arcade considering Unit's 03 and 04 are only awarded to people living in North America, like the legendary Unit 02 being exclusive to the Europeans. Either somebody traded for it, won it from the original owner, or actually lived on that continent.

Its custom beige/brown color actually looked good on the Evangelion despite its lack of visual camouflage in a city environment. It was equipped with a Progressive Axe in its hands and a Positron Beam Cannon strapped to its back. Both equally rare items but utterly useless in untrained hands. This guy was either highly skilled or very stupid, Shinji voted for the latter.

That's when it happened, Unit 04 jumped off a building with a flip and a twirl and landed hard on the street. Unit 13 fired its revolver at Unit 04 but the beige Evangelion ducked behind a building. The yellow Eva holstered its revolver and pulled one of its rocket launchers off of its back and aimed it at the building. With a pull of the trigger the building blew up, but no Evangelion was insight. Then there was a flash of beige and the rocket launcher blew up as it was sliced in half by a mighty axe.

Unit 13's right arm went limp as the appendage was damaged by the blast. It tried to grab another weapon but was soon cut in half by the Progressive Axe. The match was decided in little under a minute. Ichigo's simulator opened up and the young man was cursing up a storm. Kensuke let out a whistle.

"That guy's pretty good to beat Ichigo so easily, one of you should challenge the new guy" Shinji and Touji both looked at each other and nodded their heads. They jumped away from each other and stared one another down. They both raised their right hands in to the air and yelled out

"Rock, Paper, Scissor".

* * *

Gendo took a drink of his coffee while Kyoko sipped her tea. He was currently showing her his new vaccine for the common cold. She was intrigued by the simplicity of it.

"So using the body's own defenses…" she began to understand.

"The vaccine neutralizes the virus" Gendo stated proudly.

"That's incredible" she scooted her chair closer to Gendo to get a better view of the screen. When she looked back up at him, she realized how close they really were and backed away. Noticing her nervousness he decided to get both of them out of his office.

"How about we go upstairs and I show you our new anti-contamination plug suits" Gendo suggested.

"That'd be great" Kyoko agreed.

* * *

Shinji grinned at Touji, stepped into the simulator, and closed the hatch. He sat down in the seat and put on the neural connectors that were connected to the machine.

"Welcome to Bio-Mech: Evangelion, please insert two tokens now" Shinji grabbed two tokens from his pocket and placed them in the slot.

_Evangelion intro music (The Cruel Angels Thesis) plays._

"Select your Evangelion" Shinji looked at all the Mechs he had unlocked over the years. A few promotional ones like the Yebisu Unit 21 and the Diet LCL Cola Unit 11. He still had the basic starter Unit 00 as well as Unit's 06, 09, and 17. Yes, he played this game way too much. But in the end he selected his pride and joy. His custom purple and green Unit 01, he earned this baby from a regional champ last year and it's his most prized Evangelion.

"Select your weapons" Shinji knew he was up against a pro now, so he pulled out something he knew the challenger would like "Are you ready pilot?" the game asked and Shinji nodded his head "EVA LAUNCH" the game yelled.

Touji and Kensuke were excited, they haven't seen Shinji play in a couple months and wondered how well he'd fare against this new guy. A small loading screen appeared but was soon replaced by the fully rendered fictional city of Tokyo-3.

Unit 01 appeared from an underground launch tube and came to an abrupt stop as it reached the surface. He had his Progressive Katana in his hands and a Positron Rifle strapped to his back. He halfway expected his opponent to appear from the ground like him but he was disappointed when there was no enemy in front of him. That soon changed as he heard a plane high in the sky. Shinji let a small grin fall onto his face; even he hadn't unlocked that secret opening entrance.

'This'll be one hell of a fight' he thought to himself as the red and orange form landed on the ground with a mighty thud. He stared in shock as he got a good view of the Evangelion in front of him.

"No Freaking Way" Kensuke shouted as everybody else stood in awe at the sight before them "That's Unit 02" this was a treat for all of the spectators. Everybody knew that someone in their arcade owned a Unit 01 but now they get to see two legendary Evangelion's in action. Kensuke set up a wireless link from his camera to the game terminal. He wanted to save this for later.

Shinji let the shock pass him as he noticed that Unit 02's pilot had replaced his Progressive Axe for a Progressive Long Sword 'hell of a fight indeed' he mentally chuckled.

"Eva's ready" the game yelled out "Three" Shinji tightened his grip on the controls "Two" his opponent licked their lips in anticipation "One" everybody held their breath "Commence Battle".

The two Eva's simultaneously ran to the sides and both pulled out their Positron weapons. They quickly dodged between buildings as they both fired a single shot at one another; ammo was limited with their powerful weapons.

"Damn he's good" Shinji said as he was shot in the shoulder. It was a small hit but would slow him down a little. Unit 01 aimed at one of the buildings and pulled the trigger. The base of the building collapsed as it was shot and it began to fall on Unit 02. The red Eva backed up to escape the debris but found itself square in Unit 01's sights. The purple behemoth fired three shots at Unit 02 before his weapon overheated.

He was shocked when Unit 02 dodged the first two shots but its gun was hit by the third one, effectively blowing up the weapon. Unit 01 threw down its useless Positron Rifle and grabbed its Katana while Unit 02 grabbed its Long Sword off its back.

They both charged in and ran at each other with melee weapons poised to strike. The two weapons clashed once, twice, three times before the two Evangelion's jumped back and went at it again.

The crowd was in awe at the skill the two pilots were demonstrating. Kensuke and Touji were both happy to see that Shinji was a good as ever. Of course, Touji was still a more nimble pilot then Shinji. The two boys failed to notice that the 'champ' Ichigo was none too pleased with the performance being shown to all the spectators. In fact he was beyond livid and ready pick a fight with anybody right now, but he calmed himself so he could watch and see the outcome.

Unit 01 looked at the stump that used to be its left hand and then looked back up at Unit 02. The red Eva was still whole but had lacerations all over its body, some of them very deep. Shinji looked at his Units health gauge as well as the health for his Katana, the weapon was almost depleted, he needed to finish this fight.

Though his opponent wasn't much better off then him, he still had the advantage of two working hands. There wasn't much one could do with a stump for a hand other then smack the opponent in the face. That's when he got an idea. It was risky and it pained him to mutilate his Evangelion this way but if he wanted to win then he'd have to take drastic measures.

Unit 02 began to dash forward but suddenly stopped when Unit 01 shoved its Katana into the streets below.

"He's not giving up is he" Kensuke asked.

"I…I don't think so, it's not his style to just forfeit like that" Touji answered back as he watched the left shoulder pylon open on Unit 01. The Evangelion grabbed the default Progressive Knife and activated the weapon. A few people got sick as Unit 01 drove the blade into its own stump of an arm.

"What the hell is he doing, that's hurting his own health" Touji didn't have an answer for his sandy haired friend.

Once a hole was made, Unit 01 jammed the hilt of the knife in the hole and swung it around a few times. Shinji smiled as he wielded his secondary weapon with his bloody stump. Unit 01 pulled its Katana out of the ground and got into a unique fighting stance.

Unit 02's pilot was a little surprised at what had just happened but smirked at the new challenge it created. Unit 02 jumped onto the side of a building and climbed to the top with Unit 01 right behind it.

The two mighty Evangelion's stared each other down for a brief moment before they leaped from building to building clashing in mid air before landing on another building. Unit 01 bounded across a few stray buildings and slashed at Unit 02 with its Katana only for it to be parried by Unit 02's Long Sword. That's exactly the reaction Shinji wanted as he plunged his Knife into the stomach of Unit 02. The red Unit quickly kicked him off and Unit 01 landed hard into the ground.

Unit 02 leaped off the building after the purple monstrosity, with its blade pointed down to impale the Evangelion. Shinji now knew he wasn't going to win but at least he had fun. Unit 02 landed on Unit 01 and its sword was soon coated in blood.

The crowds cheered as the battle ended but they were soon in an uproar when the gamed yelled out "Tie Game" Kensuke quickly pointed to the two Evangelion's as Unit 02 collapsed to the ground with a Katana blade protruding from its back.

"Now that was a battle" Touji cheered as Kensuke saved the battle data to his camera, which was linked to his computer at home.

* * *

"So you have a daughter named Asuka" Gendo asked Kyoko as they walked out of Nerv.

"Yes, she's a second year student at the middle school" she informed him.

"Same as my two kids, Shinji and Rei" he told her as they reached her car "I wonder if they're in the same class".

"That'd be an interesting coincidence" Kyoko sat in her car and lowered her window "It was nice to meet you Dr. Rokubungi"

"Please Kyoko, call me Gendo" she let a small smile grace her lips.

"Okay, I'll see you tomorrow Gendo" she put up her window and drove home. Gendo watched her car until it was no longer in sight.

"It was very nice to meet you too, Kyoko" he whispered to himself and walked back to his own car. He was going to enjoy having an assistant.

* * *

"I still can't believe we tied" Asuka laughed as she and Shinji walked back to her house together.

"I'm still getting over the fact that it was you I was facing. That was the most intense battle I've had in a long time" he told the redhead honestly.

"Same here" she agreed. The rest of their walk was held in silence as the two enjoyed each other's company. When they reached her house, she gave Shinji a small wave and a smile as she closed her door.

As Shinji made his way back home, he couldn't get rid of the dumb grin plastered on his face.

* * *

Rei slowly walked back to her apartment, alone. Shinji had forgotten to pick her up from school.

'He forgot about me' she thought as she dragged her feet 'this is all that girl Asuka's fault' Rei clenched her small hands into tight fists 'I won't lose to you Soryu'.

"I'm the only woman for my _onii-chan_".

* * *

**A/N: My god, I've finally done it! I've turned Rei into Kanako. Well, at least Kanako was Keitaro's adopted sister and not his half sister.**

**I think I may have gone overboard with the Evangelion simulator scenes. I wrote most of this all in one sitting so I just let it flow out of me. Let me know if I should include more simulator battles in later chapters or if I should leave it alone.**

**As for the pairings, it's gonna be interesting. I think this may be the first official Gendo x Kyoko pairing but I could be wrong. Like the title implies, the children's relationship is going to be complicated, as well as the adults considering dating in the work place.**

**Review if you want to but it often helps when you do. Feedback is always appreciated.**

**Read ya Later.**


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